isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data

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609
Source code
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Man pages
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isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data
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API for isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data

Global functions
%inrange% Man page
.IBSpectraAsConciseDataFrameNew Source code
.NULLstring Source code
.abbrev Source code
.add.quant.to.xls.tbl Source code
.all.duplicate.rows Source code
.all.duplicates Source code
.as.matrix Source code
.as.vect Source code
.bnds Source code Source code
.build.protein.group Source code
.calc.col Source code
.calc.lm Source code
.calc.seqcov Source code
.calc.weighted.lm Source code
.calc.weighted.ratio Source code
.calc.zscore Source code Source code
.calcProbXGreaterThanY.orig Source code
.calculate.mw Source code
.call.cmd Source code
.call.estimateRatio Source code
.check.assayDataElements Source code
.check.columns Source code
.check.isfunction Source code
.check.property Source code
.cn Source code
.combine.fisher Source code
.combine.fisher.tblwide Source code
.compile.tex Source code
.concensus.il.peptide Source code
.consolidate.charge Source code
.consolidate.modification.pos Source code
.consolidate.peptide.ids Source code
.convert.msgfp.pepmodif Source code
.convert.msgfp.protein Source code
.convertModifToPhosphoRS Source code
.convertModifToPos Source code
.convertPeptideModif Source code
.convertPhosphoRSPepProb Source code
.create.or.load Source code
.create.or.load.ibspectra Source code
.create.or.load.merged.table Source code
.create.or.load.my.protein.infos Source code
.create.or.load.noise.model Source code
.create.or.load.ptm.info Source code
.create.or.load.quant.table Source code
.create.or.load.ratiodistr Source code
.create.or.load.xls.quant.tbl Source code
.create.xls.peptide.quant.tbl Source code
.create.xls.protein.quant.tbl Source code
.dissect.search.engines Source code
.do.create.protein.info Source code
.do.map Source code
.do.resolve.conflicts Source code
.exists.property Source code
.expand.w.vector Source code
.extend.protein.group Source code
.factor.as.character Source code
.factor.to.chr Source code
.fix.il.peptide Source code
.get.cmbn Source code
.get.cols Source code
.get.database Source code
.get.dupl.n.warn Source code
.get.merged.table Source code
.get.modif.pos Source code
.get.modif.pos.for.ac Source code
.get.names Source code
.get.normalization.factors Source code
.get.or.load Source code
.get.property Source code
.get.quant Source code
.get.quant.elems Source code
.get.ri Source code Source code
.get.tbl.pg Source code
.get.varMetaData Source code
.getModifOnPosition Source code
.gg_element_text Source code
.gg_theme Source code
.grep_columns Source code
.has.modif Source code
.lines.nf Source code
.lines.nm Source code
.load.property Source code
.max.uniq Source code
.mean.na.rm Source code
.merge.identifications Source code
.merge.identifications.full Source code
.merge.quant.identifications Source code
.merge.search.engine.identifications Source code
.most Source code
.moveToFirstCol Source code
.na.rm Source code
.names.as.vector Source code
.onAttach Source code
.panel.cor Source code
.panel.smooth Source code
.panel.txt Source code
.paste_unique Source code
.plot.data Source code
.plot.heatmaps Source code
.plot.heatmaps.gd Source code
.plot.pairs Source code
.print.proteinrow Source code
.protein.acc Source code
.proteinGroupAsConciseDataFrame Source code
.proteinGroupAsConciseDataFrame1 Source code
.proteinInfo.ok Source code
.proteinPtmInfo Source code
.proteins.w.shared.peptides Source code
.read.identifications Source code
.read.idfile Source code
.read.idfile.df Source code
.read.mgf Source code
.read.msgfp.tsv Source code
.read.peaklist Source code
.read.rockerbox Source code
.remove.duplications Source code
.reshapeLong Source code
.resolve.conflicts Source code
.resolve.differing.identifications Source code
.resolve.modifications Source code
.return.equal.or.na Source code
.round.distr Source code
.sanitize.sh Source code
.scatter.plot Source code
.searchengine.cols Source code
.sel.outliers Source code
.set Source code
.simplify.seqcov Source code
.stopiflengthnotequal Source code
.stopifna Source code
.stopifnot Source code
.string.number.ranges Source code
.strsplit_vector Source code
.sum.bool Source code
.sum.bool.c Source code
.sum.bool.na Source code
.summarize.pepmodif Source code
.summarize.splice.variants Source code
.take.max Source code
.tex.combinenames Source code
.trim Source code
.ttest.pval Source code
.ttest.pval.se Source code
.unique.or.collapse Source code
.valid.IBSpectra Source code
.valid.IBSpectra.slots Source code
.valid.NoiseModel Source code
.valid.NoiseModel.slots Source code
.valid.ProteinGroup Source code
.valid.ProteinGroup.slots Source code
.vector.as.data.frame Source code
.weighted.cor Source code
.write.summarized.table Source code
.write.t Source code
.write.xls.report Source code
AbscontDistribution-class Man page
Distribution-class Man page
ExponentialNoANoiseModel-class Man page
ExponentialNoiseModel-class Man page
GROUPSPECIFIC Man page
GeneralNoiseModel-class Man page
IBSpectra Man page
IBSpectra-class Man page
IBSpectraTypes Man page Source code
InverseNoANoiseModel-class Man page
InverseNoiseModel-class Man page
NoiseModel Man page
NoiseModel,IBSpectra-method Man page
NoiseModel-class Man page
Parameter-class Man page
ProteinGroup Man page Man page
ProteinGroup,data.frame,NULL-method Man page
ProteinGroup,data.frame,ProteinGroup-method Man page
ProteinGroup,data.frame,missing-method Man page
ProteinGroup-class Man page
REPORTERSPECIFIC Man page
SPECIFICITIES Man page
TMT10plexSpectra Man page
TMT10plexSpectra-class Man page
TMT2plexSpectra Man page
TMT2plexSpectra-class Man page
TMT6plexSpectra Man page
TMT6plexSpectra-class Man page
TMT6plexSpectra2 Man page
TMT6plexSpectra2-class Man page
TMTSpectra Man page
TMTSpectra-class Man page
TlsParameter-class Man page
Tlsd Man page Source code
Tlsd-class Man page
UNSPECIFIC Man page
UnivariateDistribution-class Man page
VARMETADATA Man page
adjust.ratio.pvalue Man page Source code
as.data.frame,IBSpectra-method Man page
as.data.frame,ProteinGroup-method Man page
as.data.frame.IBSpectra Man page Source code
as.data.frame.ProteinGroup Man page Source code
calc.delta.score Man page Source code
calc.pep.delta.score Man page Source code
calcCumulativeProbXGreaterThanY Man page Source code
calcPeptidePosition Man page Source code
calcProbXDiffNormals Man page Source code
calcProbXGreaterThanY Man page Source code
calculate.dNSAF Man page Source code
calculate.emPAI Man page Source code
calculate.mult.sample.pvalue Man page Source code
calculate.ratio.pvalue Man page Source code
calculate.sample.pvalue Man page Source code
class:IBSpectra Man page
class:NoiseModel Man page
class:ProteinGroup Man page
classLabels Man page
classLabels,IBSpectra-method Man page
classLabels<- Man page
classLabels<-,IBSpectra-method Man page
coerce,IBSpectra,data.frame-method Man page
coerce,data.frame,ProteinGroup-method Man page
combn.matrix Man page Source code
combn.protein.tbl Man page Source code
connect.nodes Man page Source code
correct.peptide.ratios Man page Source code
correctIsotopeImpurities Man page
correctIsotopeImpurities,IBSpectra-method Man page
create.meta.reports Man page Source code
create.reports Man page Source code
distrprint Man page Source code
do.log Man page
do.log,IBSpectra,character-method Man page
draw.boxplot Man page Source code
draw.protein.group Man page Source code
draw.proteingroup.row Man page Source code
estimateRatio Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,character-m Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,data.frame- Man page
estimateRatio,IBSpectra,ANY,character,character,NULL,matrix-meth Man page
estimateRatio,IBSpectra,ANY,character,character,character,NULL-m Man page
estimateRatio,IBSpectra,ANY,character,character,character,missin Man page
estimateRatio,IBSpectra,ANY,character,character,missing,characte Man page
estimateRatio,IBSpectra,ANY,character,character,missing,data.fra Man page
estimateRatio,IBSpectra,ANY,character,character,missing,matrix-m Man page
estimateRatio,IBSpectra,ANY,missing,missing,character,missing-me Man page
estimateRatio,IBSpectra,ANY,missing,missing,missing,character-me Man page
estimateRatioForPeptide Man page Source code
estimateRatioForProtein Man page Source code
estimateRatioNumeric Man page
estimateRatioNumeric,numeric,numeric,NULL-method Man page
estimateRatioNumeric,numeric,numeric,NoiseModel-method Man page
estimateRatioNumeric,numeric,numeric,missing-method Man page
exclude Man page
exclude,IBSpectra,character-method Man page
filterSpectraDeltaScore Man page Source code
filterSpectraPhosphoRS Man page Source code
fitCauchy Man page Source code
fitGaussianMixture Man page Source code
fitNorm Man page Source code
fitNormalCauchyMixture Man page Source code
fitTlsd Man page Source code
fitWeightedNorm Man page Source code
get.log Man page
get.log,IBSpectra,character-method Man page
get.pep.group Man page Source code
getMultUnifDensity Man page Source code
getMultUnifPValues Man page Source code
getPeptideModifContext Man page Source code
getPhosphoRSProbabilities Man page Source code
getProteinInfoFromBioDb Man page Source code
getProteinInfoFromBiomart Man page Source code
getProteinInfoFromEntrez Man page Source code
getProteinInfoFromNextProt Man page Source code
getProteinInfoFromTheInternet Man page Source code
getProteinInfoFromUniprot Man page Source code
getPtmInfoFromNextprot Man page Source code
getPtmInfoFromPhosphoSitePlus Man page Source code
get_n_proteins Man page Source code
group-specific Man page
groupMemberPeptides Man page Source code
human.protein.names Man page Source code
iTRAQ4plexSpectra Man page
iTRAQ4plexSpectra-class Man page
iTRAQ8plexSpectra Man page
iTRAQ8plexSpectra-class Man page
iTRAQSpectra Man page
iTRAQSpectra-class Man page
ibSpectra.as.concise.data.frame Man page Source code
ib_phospho Man page
ibspiked_set1 Man page
ibspiked_set2 Man page
indistinguishableProteins Man page
indistinguishableProteins,ProteinGroup,ANY,ANY-method Man page
indistinguishableProteins,ProteinGroup,character,missing-method Man page
indistinguishableProteins,ProteinGroup,missing,character-method Man page
indistinguishableProteins,ProteinGroup,missing,missing-method Man page
indistinguishableProteins,ProteinGroup-method Man page
initialize,IBSpectra-method Man page
initialize,NoiseModel-method Man page
initialize.env Man page Source code
is.logged Man page
is.logged,IBSpectra,character-method Man page
isobar Man page
isobar-analysis Man page
isobar-import Man page
isobar-package Man page
isobar-plots Man page
isobar-preprocessing Man page
isobar-reports Man page
isotopeImpurities Man page
isotopeImpurities,IBSpectra-method Man page
isotopeImpurities<- Man page
isotopeImpurities<-,IBSpectra-method Man page
load.properties Man page Source code
load.tex.properties Man page Source code
lowIntensity Man page
lowIntensity,NoiseModel-method Man page
lowIntensity<- Man page
lowIntensity<-,NoiseModel-method Man page
maplot Man page
maplot,IBSpectra,character,character-method Man page
maplot,IBSpectra,missing,missing-method Man page
maplot,missing,numeric,numeric-method Man page
maplot.protein Man page Source code
maplot2 Man page
maplot2,ANY,character,character-method Man page
maplot2,list,character,character-method Man page
modif.site.count Man page Source code
modif.sites Man page Source code
modifs Man page
my.protein.info Man page Source code
n.observable.peptides Man page Source code
naRegion Man page
naRegion,NoiseModel-method Man page
naRegion<- Man page
naRegion<-,NoiseModel-method Man page
noise.model.hcd Man page
noiseFunction Man page
noiseFunction,NoiseModel-method Man page
normalize Man page Source code
normalize,IBSpectra-method Man page
number.ranges Man page Source code
observable.peptides Man page Source code
observedKnownSites Man page Source code
parameter Man page
parameter,NoiseModel-method Man page
parameter<- Man page
parameter<-,NoiseModel-method Man page
paste0 Man page Source code
peptide.count Man page Source code
peptideInfo Man page
peptideInfo,ProteinGroup-method Man page
peptideInfo-methods Man page
peptideNProtein Man page
peptideNProtein,ProteinGroup-method Man page
peptideRatios Man page Source code
peptideRatiosNotQuant Man page Source code
peptideSpecificity Man page Man page
peptideSpecificity,ProteinGroup-method Man page Man page
peptides Man page
peptides,ProteinGroup,character-method Man page
peptides,ProteinGroup,missing-method Man page
plot.NoiseModel Man page Source code
plotRatio Man page
plotRatio,IBSpectra,character,character,character-method Man page
print_classlabels_tbl Man page Source code
print_groupsize Man page
print_longtablehdr Man page Source code
print_longtablehdr_peptide Man page Source code
print_protein_grp_info Man page Source code
print_protein_grp_tbl Man page Source code
print_protein_notquant_tbl Man page Source code
print_protein_quant_tbl Man page Source code
print_sign_proteins_tbl Man page Source code
property Man page Source code
protGgdata Man page
protGgdata,ANY,character,character-method Man page
protein.ac Man page
protein.ac,ProteinGroup,character-method Man page
protein.ac,ProteinGroup,missing-method Man page
protein.g Man page
protein.g,ProteinGroup,character,character-method Man page
protein.g,ProteinGroup,character-method Man page
proteinDescription Man page Source code
proteinGeneName Man page Source code
proteinGroup Man page
proteinGroup,IBSpectra-method Man page
proteinGroup.as.concise.data.frame Man page Source code
proteinGroup<- Man page
proteinGroup<-,IBSpectra-method Man page
proteinGroupTable Man page
proteinGroupTable,ProteinGroup-method Man page
proteinID Man page Source code
proteinInfo Man page
proteinInfo,ProteinGroup,character,missing-method Man page
proteinInfo,ProteinGroup,missing,character-method Man page
proteinInfo,ProteinGroup,missing,missing-method Man page
proteinInfo,ProteinGroup-method Man page
proteinInfo-methods Man page
proteinInfo<- Man page
proteinInfo<-,ProteinGroup-method Man page
proteinInfoIsOnSpliceVariants Man page Source code
proteinNameAndDescription Man page Source code
proteinRatios Man page Source code
raplot Man page
raplot,IBSpectra-method Man page
ratiosReshapeWide Man page Source code
read.mzid Man page Source code
readIBSpectra Man page
readIBSpectra,character,character,character-method Man page
readIBSpectra,character,character,missing-method Man page
readIBSpectra,character,character-method Man page
readIBSpectra,character,data.frame,character-method Man page
readIBSpectra,character,data.frame,missing-method Man page
readPhosphoRSOutput Man page Source code
readProteinGroup Man page Source code
readProteinGroup2 Man page Source code
reporter-specific Man page
reporter.protein Man page
reporter.protein,ProteinGroup,character-method Man page
reporter.protein-methods Man page
reporterData Man page
reporterData,IBSpectra-method Man page
reporterData<- Man page
reporterData<-,IBSpectra-method Man page
reporterIntensities Man page
reporterIntensities,IBSpectra-method Man page
reporterIntensities<- Man page
reporterIntensities<-,IBSpectra-method Man page
reporterIntensityPlot Man page
reporterIntensityPlot,IBSpectra-method Man page
reporterIntensityPlot-methods Man page
reporterMassPrecision Man page
reporterMassPrecision,IBSpectra,logical-method Man page
reporterMassPrecision,IBSpectra,missing-method Man page
reporterMasses Man page
reporterMasses,IBSpectra-method Man page
reporterMasses<- Man page
reporterMasses<-,IBSpectra-method Man page
reporterProteins Man page
reporterProteins,ProteinGroup-method Man page
reporterTagMasses Man page
reporterTagMasses,IBSpectra-method Man page
reporterTagNames Man page
reporterTagNames,IBSpectra-method Man page
sanitize Man page Source code
sequence.coverage Man page Source code
shared.ratios Man page Source code
shared.ratios.sign Man page Source code
show,IBSpectra-method Man page
show,NoiseModel-method Man page
show,ProteinGroup-method Man page
specificities Man page
spectra.count Man page Source code
spectra.count2 Man page Source code
spectrumSel Man page
spectrumSel,IBSpectra,character,missing-method Man page
spectrumSel,IBSpectra,data.frame,missing-method Man page
spectrumSel,IBSpectra,matrix,missing-method Man page
spectrumSel,IBSpectra,missing,character-method Man page
spectrumSel,IBSpectra,missing,missing-method Man page
spectrumTitles Man page
spectrumTitles,IBSpectra-method Man page
spectrumToPeptide Man page
spectrumToPeptide,ProteinGroup-method Man page
stddev Man page
stddev,NoiseModel-method Man page
subsetIBSpectra Man page Source code
subtractAdditiveNoise Man page
subtractAdditiveNoise,IBSpectra-method Man page
summarize.ratios Man page Source code
summary.ProteinGroup Man page Source code
testPdflatex Man page Source code
testPerl Man page Source code
tikz.proteingroup Man page Source code
transform_pepmodif Man page Source code
twodistr.plot Man page Source code
unspecific Man page
variance Man page
variance,NoiseModel,numeric,missing-method Man page
variance,NoiseModel,numeric,numeric-method Man page
weightedMean Man page
weightedMean,numeric,numeric-method Man page
weightedVariance Man page
weightedVariance,numeric,numeric,missing-method Man page
weightedVariance,numeric,numeric,numeric-method Man page
write.tex.commands Man page Source code
write.xls.report Man page Source code
writeData Man page Source code
writeData,IBSpectra-method Man page
writeHscoreData Man page Source code
writeIBSpectra Man page Source code
writePhosphoRSInput Man page Source code
isobar documentation built on Nov. 8, 2020, 7:48 p.m.

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